72 #define NCBI_USE_ERRCODE_X Objtools_Rd_RepMask
124 ERR_POST(
Info <<
" CFormatGuessEx:: Initial CFormatGuess: " << (
int)Guess);
145 for(
size_t loop = 0; loop < checkCount; loop++ ) {
146 auto CheckFormat = CheckOrder[loop];
175 streamsize Total = 0;
178 In.read(buff,
sizeof(buff));
179 streamsize
count = In.gcount();
184 if(Total >= (1024*1024))
272 return (!Bioseqs.empty());
289 Annot =
Reader.ReadSeqAnnot(LineReader);
299 return (WiggleCount > 0);
312 list<CRef<CSeq_annot> > LocalAnnots;
314 Reader.ReadSeqAnnots(LocalAnnots, LineReader);
320 if(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&
321 (*AnnotIter)->GetData().IsFtable())
325 return (BedCount > 0);
340 Annot =
Reader.ReadSeqAnnot(LineReader);
350 return (Bed15Count > 0);
361 Result =
Reader.ReadSet(1);
385 Reader.ReadSeqAnnots(LocalAnnots, LineReader);
391 if(!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
392 (**AnnotIter).GetData().IsFtable())
396 return (GtfCount > 0);
411 Reader.ReadSeqAnnots(LocalAnnots, LineReader);
417 if (!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
418 (**AnnotIter).GetData().IsFtable())
422 return (Gff3Count > 0);
437 Reader.ReadSeqAnnots(LocalAnnots, LineReader);
443 if (!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
444 (**AnnotIter).IsFtable())
448 return (Gff2Count > 0);
455 unique_ptr<CObjectIStream> pObjStream;
475 if( !pObjStream.get() ) {
480 if (
types.size() != 1 ) {
483 return *
types.begin();
487 const set<TTypeInfo>& recognizedGenbankTypes)
496 switch (baseFormat) {
User-defined methods of the data storage class.
virtual int ReadStream(CNcbiIstream &is, EFinalize eFinalize=eFinalize_Yes)
Read an AGP file from the given input stream.
This class is used to turn an AGP file into a vector of Seq-entry's.
vector< CRef< objects::CSeq_entry > > TSeqEntryRefVec
This is the way the results will be returned Each Seq-entry contains just one Bioseq,...
TSeqEntryRefVec & GetResult(void)
This gets the results found, but don't call before finalizing.
CReaderBase implementation that reads BED data files, either a single object or all objects found.
CObjectIStreamAsnBinary –.
Implements a concrete class for reading RepeatMasker output from tabular form and rendering it as ASN...
Simple implementation of ILineReader for i(o)streams.
CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...
@ fIncludeRepeatClass
Same as fIncludeRepeatFamily.
Include a standard set of the NCBI C++ Toolkit most basic headers.
Operators to edit gaps in sequences.
static void TestResult(SQLRETURN result0, int level, const char *func)
static const struct type types[]
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
@ eNoOwnership
No ownership is assumed.
#define ERR_POST(message)
Error posting with file, line number information but without error codes.
void Info(CExceptionArgs_Base &args)
static TTypeInfo GetTypeInfo(void)
bool NotEmpty(void) const THROWS_NONE
Check if CRef is not empty – pointing to an object and has a non-null value.
bool IsNull(void) const THROWS_NONE
Check if pointer is null – same effect as Empty().
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static void Pushback(CNcbiIstream &is, CT_CHAR_TYPE *buf, streamsize buf_size, void *del_ptr)
IO_PREFIX::istream CNcbiIstream
Portable alias for istream.
IO_PREFIX::ifstream CNcbiIfstream
Portable alias for ifstream.
const string & GetName(void) const
Get name of this type.
const TSet & GetSet(void) const
Get the variant data.
bool IsSet(void) const
Check if variant Set is selected.
const TSeq_set & GetSeq_set(void) const
Get the Seq_set member data.
bool IsFtable(void) const
Check if variant Ftable is selected.
const TData & GetData(void) const
Get the Data member data.
bool CanGetData(void) const
Check if it is safe to call GetData method.
Lightweight interface for getting lines of data with minimal memory copying.
Magic spell ;-) needed for some weird compilers... very empiric.
GenericReader< UTF8< char >, UTF8< char >, CrtAllocator > Reader
Reader with UTF8 encoding and default allocator.
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
Defines NCBI C++ exception handling.
Multi-threading – classes, functions, and features.
Useful/utility classes and methods.
CFileContentInfoGff3 mInfoGff3
CFileContentInfoNone mInfoNone
CFileContentInfoAlign mInfoAlign
CFileContentInfoGenbank mInfoGenbank